With the directory listing on the web, we can directly get access to the output files and navigate what output that we have, I guess. If there are other options about managing multiple output files, I really want to hear about that.

Hopefully collections will be able to solve this problem within the next few releases but currently tools cannot create collections. There is an open Trello card for that feature here https://trello.com/c/KXjp6lIn.

In the meantime - I think the two options (both with admittedly serious limitations) are runtime collected datasets and composite datatypes are outlined on the wiki page linked to in the question.